Displaying 1 - 27 of 27
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Carrion Castillo, A., Van der Haegen, L., Tzourio-Mazoyer, N., Kavaklioglu, T., Badillo, S., Chavent, M., Saracco, J., Brysbaert, M., Fisher, S. E., Mazoyer, B., & Francks, C. (2019). Genome sequencing for rightward hemispheric language dominance. Genes, Brain and Behavior, 18(5): e12572. doi:10.1111/gbb.12572.
Abstract
Most people have left‐hemisphere dominance for various aspects of language processing, but only roughly 1% of the adult population has atypically reversed, rightward hemispheric language dominance (RHLD). The genetic‐developmental program that underlies leftward language laterality is unknown, as are the causes of atypical variation. We performed an exploratory whole‐genome‐sequencing study, with the hypothesis that strongly penetrant, rare genetic mutations might sometimes be involved in RHLD. This was by analogy with situs inversus of the visceral organs (left‐right mirror reversal of the heart, lungs and so on), which is sometimes due to monogenic mutations. The genomes of 33 subjects with RHLD were sequenced and analyzed with reference to large population‐genetic data sets, as well as 34 subjects (14 left‐handed) with typical language laterality. The sample was powered to detect rare, highly penetrant, monogenic effects if they would be present in at least 10 of the 33 RHLD cases and no controls, but no individual genes had mutations in more than five RHLD cases while being un‐mutated in controls. A hypothesis derived from invertebrate mechanisms of left‐right axis formation led to the detection of an increased mutation load, in RHLD subjects, within genes involved with the actin cytoskeleton. The latter finding offers a first, tentative insight into molecular genetic influences on hemispheric language dominance.Additional information
gbb12572-sup-0001-AppendixS1.docx -
Eising, E., Carrion Castillo, A., Vino, A., Strand, E. A., Jakielski, K. J., Scerri, T. S., Hildebrand, M. S., Webster, R., Ma, A., Mazoyer, B., Francks, C., Bahlo, M., Scheffer, I. E., Morgan, A. T., Shriberg, L. D., & Fisher, S. E. (2019). A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development. Molecular Psychiatry, 24, 1065-1078. doi:10.1038/s41380-018-0020-x.
Abstract
Genetic investigations of people with impaired development of spoken language provide windows into key aspects of human biology. Over 15 years after FOXP2 was identified, most speech and language impairments remain unexplained at the molecular level. We sequenced whole genomes of nineteen unrelated individuals diagnosed with childhood apraxia of speech, a rare disorder enriched for causative mutations of large effect. Where DNA was available from unaffected parents, we discovered de novo mutations, implicating genes, including CHD3, SETD1A and WDR5. In other probands, we identified novel loss-of-function variants affecting KAT6A, SETBP1, ZFHX4, TNRC6B and MKL2, regulatory genes with links to neurodevelopment. Several of the new candidates interact with each other or with known speech-related genes. Moreover, they show significant clustering within a single co-expression module of genes highly expressed during early human brain development. This study highlights gene regulatory pathways in the developing brain that may contribute to acquisition of proficient speech.Additional information
Eising_etal_2018sup.pdf -
Francks, C. (2019). In search of the biological roots of typical and atypical human brain asymmetry. Physics of Life Reviews, 30, 22-24. doi:10.1016/j.plrev.2019.07.004.
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Francks, C. (2019). The genetic bases of brain lateralization. In P. Hagoort (
Ed. ), Human language: From genes and brain to behavior (pp. 595-608). Cambridge, MA: MIT Press. -
Gialluisi, A., Andlauer, T. F. M., Mirza-Schreiber, N., Moll, K., Becker, J., Hoffmann, P., Ludwig, K. U., Czamara, D., St Pourcain, B., Brandler, W., Honbolygó, F., Tóth, D., Csépe, V., Huguet, G., Morris, A. P., Hulslander, J., Willcutt, E. G., DeFries, J. C., Olson, R. K., Smith, S. D. and 25 moreGialluisi, A., Andlauer, T. F. M., Mirza-Schreiber, N., Moll, K., Becker, J., Hoffmann, P., Ludwig, K. U., Czamara, D., St Pourcain, B., Brandler, W., Honbolygó, F., Tóth, D., Csépe, V., Huguet, G., Morris, A. P., Hulslander, J., Willcutt, E. G., DeFries, J. C., Olson, R. K., Smith, S. D., Pennington, B. F., Vaessen, A., Maurer, U., Lyytinen, H., Peyrard-Janvid, M., Leppänen, P. H. T., Brandeis, D., Bonte, M., Stein, J. F., Talcott, J. B., Fauchereau, F., Wilcke, A., Francks, C., Bourgeron, T., Monaco, A. P., Ramus, F., Landerl, K., Kere, J., Scerri, T. S., Paracchini, S., Fisher, S. E., Schumacher, J., Nöthen, M. M., Müller-Myhsok, B., & Schulte-Körne, G. (2019). Genome-wide association scan identifies new variants associated with a cognitive predictor of dyslexia. Translational Psychiatry, 9(1): 77. doi:10.1038/s41398-019-0402-0.
Abstract
Developmental dyslexia (DD) is one of the most prevalent learning disorders, with high impact on school and psychosocial development and high comorbidity with conditions like attention-deficit hyperactivity disorder (ADHD), depression, and anxiety. DD is characterized by deficits in different cognitive skills, including word reading, spelling, rapid naming, and phonology. To investigate the genetic basis of DD, we conducted a genome-wide association study (GWAS) of these skills within one of the largest studies available, including nine cohorts of reading-impaired and typically developing children of European ancestry (N = 2562–3468). We observed a genome-wide significant effect (p < 1 × 10−8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2, within MIR924HG (micro-RNA 924 host gene; rs17663182 p = 4.73 × 10−9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; rs16928927, p = 2.25 × 10−8). rs17663182 (18q12.2) also showed genome-wide significant multivariate associations with RAN measures (p = 1.15 × 10−8) and with all the cognitive traits tested (p = 3.07 × 10−8), suggesting (relational) pleiotropic effects of this variant. A polygenic risk score (PRS) analysis revealed significant genetic overlaps of some of the DD-related traits with educational attainment (EDUyears) and ADHD. Reading and spelling abilities were positively associated with EDUyears (p ~ [10−5–10−7]) and negatively associated with ADHD PRS (p ~ [10−8−10−17]). This corroborates a long-standing hypothesis on the partly shared genetic etiology of DD and ADHD, at the genome-wide level. Our findings suggest new candidate DD susceptibility genes and provide new insights into the genetics of dyslexia and its comorbities.Additional information
https://www.nature.com/articles/s41398-019-0402-0#Sec17 -
De Kovel, C. G. F., Carrion Castillo, A., & Francks, C. (2019). A large-scale population study of early life factors influencing left-handedness. Scientific Reports, 9: 584. doi:10.1038/s41598-018-37423-8.
Abstract
Hand preference is a conspicuous variation in human behaviour, with a worldwide proportion of around 90% of people preferring to use the right hand for many tasks, and 10% the left hand. We used the large cohort of the UK biobank (~500,000 participants) to study possible relations between early life factors and adult hand preference. The probability of being left-handed was affected by the year and location of birth, likely due to cultural effects. In addition, hand preference was affected by birthweight, being part of a multiple birth, season of birth, breastfeeding, and sex, with each effect remaining significant after accounting for all others. Analysis of genome-wide genotype data showed that left-handedness was very weakly heritable, but shared no genetic basis with birthweight. Although on average left-handers and right-handers differed for a number of early life factors, all together these factors had only a minimal predictive value for individual hand preference.Additional information
Supplementary information -
De Kovel, C. G. F., Aftanas, L., Aleman, A., Alexander-Bloch, A. F., Baune, B. T., Brack, I., Bülow, R., Filho, G. B., Carballedo, A., Connolly, C. G., Cullen, K. R., Dannlowski, U., Davey, C. G., Dima, D., Dohm, K., Erwin-Grabner, T., Frodl, T., Fu, C. H., Hall, G. B., Glahn, D. C. and 58 moreDe Kovel, C. G. F., Aftanas, L., Aleman, A., Alexander-Bloch, A. F., Baune, B. T., Brack, I., Bülow, R., Filho, G. B., Carballedo, A., Connolly, C. G., Cullen, K. R., Dannlowski, U., Davey, C. G., Dima, D., Dohm, K., Erwin-Grabner, T., Frodl, T., Fu, C. H., Hall, G. B., Glahn, D. C., Godlewska, B., Gotlib, I. H., Goya-Maldonado, R., Grabe, H. J., Groenewold, N. A., Grotegerd, D., Gruber, O., Harris, M. A., Harrison, B. J., Hatton, S. N., Hickie, I. B., Ho, T. C., Jahanshad, N., Kircher, T., Krämer, B., Krug, A., Lagopoulos, J., Leehr, E. J., Li, M., MacMaster, F. P., MacQueen, G., McIntosh, A. M., McLellan, Q., Medland, S. E., Mueller, B. A., Nenadic, I., Osipov, E., Papmeyer, M., Portella, M. J., Reneman, L., Rosa, P. G., Sacchet, M. D., Schnell, K., Schrantee, A., Sim, K., Simulionyte, E., Sindermann, L., Singh, A., Stein, D. J., Ubani, B. N., der Wee, N. J. V., der Werff, S. J. V., Veer, I. M., Vives-Gilabert, Y., Völzke, H., Walter, H., Walter, M., Schreiner, M. W., Whalley, H., Winter, N., Wittfeld, K., Yang, T. T., Yüksel, D., Zaremba, D., Thompson, P. M., Veltman, D. J., Schmaal, L., & Francks, C. (2019). No alterations of brain structural asymmetry in major depressive disorder: An ENIGMA consortium analysis. American Journal of Psychiatry, 176(12), 1039-1049. doi:10.1176/appi.ajp.2019.18101144.
Abstract
Objective:
Asymmetry is a subtle but pervasive aspect of the human brain, and it may be altered in several psychiatric conditions. MRI studies have shown subtle differences of brain anatomy between people with major depressive disorder and healthy control subjects, but few studies have specifically examined brain anatomical asymmetry in relation to this disorder, and results from those studies have remained inconclusive. At the functional level, some electroencephalography studies have indicated left fronto-cortical hypoactivity and right parietal hypoactivity in depressive disorders, so aspects of lateralized anatomy may also be affected. The authors used pooled individual-level data from data sets collected around the world to investigate differences in laterality in measures of cortical thickness, cortical surface area, and subcortical volume between individuals with major depression and healthy control subjects.
Methods:
The authors investigated differences in the laterality of thickness and surface area measures of 34 cerebral cortical regions in 2,256 individuals with major depression and 3,504 control subjects from 31 separate data sets, and they investigated volume asymmetries of eight subcortical structures in 2,540 individuals with major depression and 4,230 control subjects from 32 data sets. T1-weighted MRI data were processed with a single protocol using FreeSurfer and the Desikan-Killiany atlas. The large sample size provided 80% power to detect effects of the order of Cohen’s d=0.1.
Results:
The largest effect size (Cohen’s d) of major depression diagnosis was 0.085 for the thickness asymmetry of the superior temporal cortex, which was not significant after adjustment for multiple testing. Asymmetry measures were not significantly associated with medication use, acute compared with remitted status, first episode compared with recurrent status, or age at onset.
Conclusions:
Altered brain macro-anatomical asymmetry may be of little relevance to major depression etiology in most cases. -
De Kovel, C. G. F., & Francks, C. (2019). The molecular genetics of hand preference revisited. Scientific Reports, 9: 5986. doi:10.1038/s41598-019-42515-0.
Abstract
Hand preference is a prominent behavioural trait linked to human brain asymmetry. A handful of genetic variants have been reported to associate with hand preference or quantitative measures related to it. Most of these reports were on the basis of limited sample sizes, by current standards for genetic analysis of complex traits. Here we performed a genome-wide association analysis of hand preference in the large, population-based UK Biobank cohort (N = 331,037). We used gene-set enrichment analysis to investigate whether genes involved in visceral asymmetry are particularly relevant to hand preference, following one previous report. We found no evidence supporting any of the previously suggested variants or genes, nor that genes involved in visceral laterality have a role in hand preference. It remains possible that some of the previously reported genes or pathways are relevant to hand preference as assessed in other ways, or else are relevant within specific disorder populations. However, some or all of the earlier findings are likely to be false positives, and none of them appear relevant to hand preference as defined categorically in the general population. Our analysis did produce a small number of novel, significant associations, including one implicating the microtubule-associated gene MAP2 in handedness. -
Postema, M., Van Rooij, D., Anagnostou, E., Arango, C., Auzias, G., Behrmann, M., Busatto Filho, G., Calderoni, S., Calvo, R., Daly, E., Deruelle, C., Di Martino, A., Dinstein, I., Duran, F. L. S., Durston, S., Ecker, C., Ehrlich, S., Fair, D., Fedor, J., Feng, X. and 38 morePostema, M., Van Rooij, D., Anagnostou, E., Arango, C., Auzias, G., Behrmann, M., Busatto Filho, G., Calderoni, S., Calvo, R., Daly, E., Deruelle, C., Di Martino, A., Dinstein, I., Duran, F. L. S., Durston, S., Ecker, C., Ehrlich, S., Fair, D., Fedor, J., Feng, X., Fitzgerald, J., Floris, D. L., Freitag, C. M., Gallagher, L., Glahn, D. C., Gori, I., Haar, S., Hoekstra, L., Jahanshad, N., Jalbrzikowski, M., Janssen, J., King, J. A., Kong, X., Lazaro, L., Lerch, J. P., Luna, B., Martinho, M. M., McGrath, J., Medland, S. E., Muratori, F., Murphy, C. M., Murphy, D. G. M., O'Hearn, K., Oranje, B., Parellada, M., Puig, O., Retico, A., Rosa, P., Rubia, K., Shook, D., Taylor, M., Tosetti, M., Wallace, G. L., Zhou, F., Thompson, P., Fisher, S. E., Buitelaar, J. K., & Francks, C. (2019). Altered structural brain asymmetry in autism spectrum disorder in a study of 54 datasets. Nature Communications, 10: 4958. doi:10.1038/s41467-019-13005-8.
Additional information
Supplementary Information -
Satizabal, C. L., Adams, H. H. H., Hibar, D. P., White, C. C., Knol, M. J., Stein, J. L., Scholz, M., Sargurupremraj, M., Jahanshad, N., Roshchupkin, G. V., Smith, A. V., Bis, J. C., Jian, X., Luciano, M., Hofer, E., Teumer, A., Van der Lee, S. J., Yang, J., Yanek, L. R., Lee, T. V. and 271 moreSatizabal, C. L., Adams, H. H. H., Hibar, D. P., White, C. C., Knol, M. J., Stein, J. L., Scholz, M., Sargurupremraj, M., Jahanshad, N., Roshchupkin, G. V., Smith, A. V., Bis, J. C., Jian, X., Luciano, M., Hofer, E., Teumer, A., Van der Lee, S. J., Yang, J., Yanek, L. R., Lee, T. V., Li, S., Hu, Y., Koh, J. Y., Eicher, J. D., Desrivières, S., Arias-Vasquez, A., Chauhan, G., Athanasiu, L., Renteria, M. E., Kim, S., Höhn, D., Armstrong, N. J., Chen, Q., Holmes, A. J., Den Braber, A., Kloszewska, I., Andersson, M., Espeseth, T., Grimm, O., Abramovic, L., Alhusaini, S., Milaneschi, Y., Papmeyer, M., Axelsson, T., Ehrlich, S., Roiz-Santiañez, R., Kraemer, B., Håberg, A. K., Jones, H. J., Pike, G. B., Stein, D. J., Stevens, A., Bralten, J., Vernooij, M. W., Harris, T. B., Filippi, I., Witte, A. V., Guadalupe, T., Wittfeld, K., Mosley, T. H., Becker, J. T., Doan, N. T., Hagenaars, S. P., Saba, Y., Cuellar-Partida, G., Amin, N., Hilal, S., Nho, K., Karbalai, N., Arfanakis, K., Becker, D. M., Ames, D., Goldman, A. L., Lee, P. H., Boomsma, D. I., Lovestone, S., Giddaluru, S., Le Hellard, S., Mattheisen, M., Bohlken, M. M., Kasperaviciute, D., Schmaal, L., Lawrie, S. M., Agartz, I., Walton, E., Tordesillas-Gutierrez, D., Davies, G. E., Shin, J., Ipser, J. C., Vinke, L. N., Hoogman, M., Jia, T., Burkhardt, R., Klein, M., Crivello, F., Janowitz, D., Carmichael, O., Haukvik, U. K., Aribisala, B. S., Schmidt, H., Strike, L. T., Cheng, C.-Y., Risacher, S. L., Pütz, B., Fleischman, D. A., Assareh, A. A., Mattay, V. S., Buckner, R. L., Mecocci, P., Dale, A. M., Cichon, S., Boks, M. P., Matarin, M., Penninx, B. W. J. H., Calhoun, V. D., Chakravarty, M. M., Marquand, A., Macare, C., Masouleh, S. K., Oosterlaan, J., Amouyel, P., Hegenscheid, K., Rotter, J. I., Schork, A. J., Liewald, D. C. M., De Zubicaray, G. I., Wong, T. Y., Shen, L., Sämann, P. G., Brodaty, H., Roffman, J. L., De Geus, E. J. C., Tsolaki, M., Erk, S., Van Eijk, K. R., Cavalleri, G. L., Van der Wee, N. J. A., McIntosh, A. M., Gollub, R. L., Bulayeva, K. B., Bernard, M., Richards, J. S., Himali, J. J., Loeffler, M., Rommelse, N., Hoffmann, W., Westlye, L. T., Valdés Hernández, M. C., Hansell, N. K., Van Erp, T. G. M., Wolf, C., Kwok, J. B. J., Vellas, B., Heinz, A., Olde Loohuis, L. M., Delanty, N., Ho, B.-C., Ching, C. R. K., Shumskaya, E., Singh, B., Hofman, A., Van der Meer, D., Homuth, G., Psaty, B. M., Bastin, M., Montgomery, G. W., Foroud, T. M., Reppermund, S., Hottenga, J.-J., Simmons, A., Meyer-Lindenberg, A., Cahn, W., Whelan, C. D., Van Donkelaar, M. M. J., Yang, Q., Hosten, N., Green, R. C., Thalamuthu, A., Mohnke, S., Hulshoff Pol, H. E., Lin, H., Jack Jr., C. R., Schofield, P. R., Mühleisen, T. W., Maillard, P., Potkin, S. G., Wen, W., Fletcher, E., Toga, A. W., Gruber, O., Huentelman, M., Smith, G. D., Launer, L. J., Nyberg, L., Jönsson, E. G., Crespo-Facorro, B., Koen, N., Greve, D., Uitterlinden, A. G., Weinberger, D. R., Steen, V. M., Fedko, I. O., Groenewold, N. A., Niessen, W. J., Toro, R., Tzourio, C., Longstreth Jr., W. T., Ikram, M. K., Smoller, J. W., Van Tol, M.-J., Sussmann, J. E., Paus, T., Lemaître, H., Schroeter, M. L., Mazoyer, B., Andreassen, O. A., Holsboer, F., Depondt, C., Veltman, D. J., Turner, J. A., Pausova, Z., Schumann, G., Van Rooij, D., Djurovic, S., Deary, I. J., McMahon, K. L., Müller-Myhsok, B., Brouwer, R. M., Soininen, H., Pandolfo, M., Wassink, T. H., Cheung, J. W., Wolfers, T., Martinot, J.-L., Zwiers, M. P., Nauck, M., Melle, I., Martin, N. G., Kanai, R., Westman, E., Kahn, R. S., Sisodiya, S. M., White, T., Saremi, A., Van Bokhoven, H., Brunner, H. G., Völzke, H., Wright, M. J., Van 't Ent, D., Nöthen, M. M., Ophoff, R. A., Buitelaar, J. K., Fernández, G., Sachdev, P. S., Rietschel, M., Van Haren, N. E. M., Fisher, S. E., Beiser, A. S., Francks, C., Saykin, A. J., Mather, K. A., Romanczuk-Seiferth, N., Hartman, C. A., DeStefano, A. L., Heslenfeld, D. J., Weiner, M. W., Walter, H., Hoekstra, P. J., Nyquist, P. A., Franke, B., Bennett, D. A., Grabe, H. J., Johnson, A. D., Chen, C., Van Duijn, C. M., Lopez, O. L., Fornage, M., Wardlaw, J. A., Schmidt, R., DeCarli, C., De Jager, P. L., Villringer, A., Debette, S., Gudnason, V., Medland, S. E., Shulman, J. M., Thompson, P. M., Seshadri, S., & Ikram, M. A. (2019). Genetic architecture of subcortical brain structures in 38,854 individuals worldwide. Nature Genetics, 51, 1624-1636. doi:10.1038/s41588-019-0511-y.
Abstract
Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease. -
Truong, D. T., Adams, A. K., Paniagua, S., Frijters, J. C., Boada, R., Hill, D. E., Lovett, M. W., Mahone, E. M., Willcutt, E. G., Wolf, M., Defries, J. C., Gialluisi, A., Francks, C., Fisher, S. E., Olson, R. K., Pennington, B. F., Smith, S. D., Bosson-Heenan, J., & Gruen, J. R. (2019). Multivariate genome-wide association study of rapid automatised naming and rapid alternating stimulus in Hispanic American and African–American youth. Journal of Medical Genetics, 56(8), 557-566. doi:10.1136/jmedgenet-2018-105874.
Abstract
Background Rapid automatised naming (RAN) and rapid alternating stimulus (RAS) are reliable predictors of reading disability. The underlying biology of reading disability is poorly understood. However, the high correlation among RAN, RAS and reading could be attributable to shared genetic factors that contribute to common biological mechanisms.
Objective To identify shared genetic factors that contribute to RAN and RAS performance using a multivariate approach.
Methods We conducted a multivariate genome-wide association analysis of RAN Objects, RAN Letters and RAS Letters/Numbers in a sample of 1331 Hispanic American and African–American youth. Follow-up neuroimaging genetic analysis of cortical regions associated with reading ability in an independent sample and epigenetic examination of extant data predicting tissue-specific functionality in the brain were also conducted.
Results Genome-wide significant effects were observed at rs1555839 (p=4.03×10−8) and replicated in an independent sample of 318 children of European ancestry. Epigenetic analysis and chromatin state models of the implicated 70 kb region of 10q23.31 support active transcription of the gene RNLS in the brain, which encodes a catecholamine metabolising protein. Chromatin contact maps of adult hippocampal tissue indicate a potential enhancer–promoter interaction regulating RNLS expression. Neuroimaging genetic analysis in an independent, multiethnic sample (n=690) showed that rs1555839 is associated with structural variation in the right inferior parietal lobule.
Conclusion This study provides support for a novel trait locus at chromosome 10q23.31 and proposes a potential gene–brain–behaviour relationship for targeted future functional analysis to understand underlying biological mechanisms for reading disability.Additional information
Supplementary data -
Carrion Castillo, A., Maassen, B., Franke, B., Heister, A., Naber, M., Van der Leij, A., Francks, C., & Fisher, S. E. (2017). Association analysis of dyslexia candidate genes in a Dutch longitudinal sample. European Journal of Human Genetics, 25(4), 452-460. doi:10.1038/ejhg.2016.194.
Abstract
Dyslexia is a common specific learning disability with a substantive genetic component. Several candidate genes have been proposed to be implicated in dyslexia susceptibility, such as DYX1C1, ROBO1, KIAA0319, and DCDC2. Associations with variants in these genes have also been reported with a variety of psychometric measures tapping into the underlying processes that might be impaired in dyslexic people. In this study, we first conducted a literature review to select single nucleotide polymorphisms (SNPs) in dyslexia candidate genes that had been repeatedly implicated across studies. We then assessed the SNPs for association in the richly phenotyped longitudinal data set from the Dutch Dyslexia Program. We tested for association with several quantitative traits, including word and nonword reading fluency, rapid naming, phoneme deletion, and nonword repetition. In this, we took advantage of the longitudinal nature of the sample to examine if associations were stable across four educational time-points (from 7 to 12 years). Two SNPs in the KIAA0319 gene were nominally associated with rapid naming, and these associations were stable across different ages. Genetic association analysis with complex cognitive traits can be enriched through the use of longitudinal information on trait development.Additional information
ejhg2016194x1.pdf The genotypic and phenotypic data have been deposited at The Language Archive -
Chen, X. S., Reader, R. H., Hoischen, A., Veltman, J. A., Simpson, N. H., Francks, C., Newbury, D. F., & Fisher, S. E. (2017). Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Scientific Reports, 7: 46105. doi:10.1038/srep46105.
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation. -
Gialluisi, A., Guadalupe, T., Francks, C., & Fisher, S. E. (2017). Neuroimaging genetic analyses of novel candidate genes associated with reading and language. Brain and Language, 172, 9-15. doi:10.1016/j.bandl.2016.07.002.
Abstract
Neuroimaging measures provide useful endophenotypes for tracing genetic effects on reading and language. A recent Genome-Wide Association Scan Meta-Analysis (GWASMA) of reading and language skills (N = 1862) identified strongest associations with the genes CCDC136/FLNC and RBFOX2. Here, we follow up the top findings from this GWASMA, through neuroimaging genetics in an independent sample of 1275 healthy adults. To minimize multiple-testing, we used a multivariate approach, focusing on cortical regions consistently implicated in prior literature on developmental dyslexia and language impairment. Specifically, we investigated grey matter surface area and thickness of five regions selected a priori: middle temporal gyrus (MTG); pars opercularis and pars triangularis in the inferior frontal gyrus (IFG-PO and IFG-PT); postcentral parietal gyrus (PPG) and superior temporal gyrus (STG). First, we analysed the top associated polymorphisms from the reading/language GWASMA: rs59197085 (CCDC136/FLNC) and rs5995177 (RBFOX2). There was significant multivariate association of rs5995177 with cortical thickness, driven by effects on left PPG, right MTG, right IFG (both PO and PT), and STG bilaterally. The minor allele, previously associated with reduced reading-language performance, showed negative effects on grey matter thickness. Next, we performed exploratory gene-wide analysis of CCDC136/FLNC and RBFOX2; no other associations surpassed significance thresholds. RBFOX2 encodes an important neuronal regulator of alternative splicing. Thus, the prior reported association of rs5995177 with reading/language performance could potentially be mediated by reduced thickness in associated cortical regions. In future, this hypothesis could be tested using sufficiently large samples containing both neuroimaging data and quantitative reading/language scores from the same individuals.Additional information
mmc1.docx -
Guadalupe, T., Mathias, S. R., Van Erp, T. G. M., Whelan, C. D., Zwiers, M. P., Abe, Y., Abramovic, L., Agartz, I., Andreassen, O. A., Arias-Vásquez, A., Aribisala, B. S., Armstrong, N. J., Arolt, V., Artiges, E., Ayesa-Arriola, R., Baboyan, V. G., Banaschewski, T., Barker, G., Bastin, M. E., Baune, B. T. and 141 moreGuadalupe, T., Mathias, S. R., Van Erp, T. G. M., Whelan, C. D., Zwiers, M. P., Abe, Y., Abramovic, L., Agartz, I., Andreassen, O. A., Arias-Vásquez, A., Aribisala, B. S., Armstrong, N. J., Arolt, V., Artiges, E., Ayesa-Arriola, R., Baboyan, V. G., Banaschewski, T., Barker, G., Bastin, M. E., Baune, B. T., Blangero, J., Bokde, A. L., Boedhoe, P. S., Bose, A., Brem, S., Brodaty, H., Bromberg, U., Brooks, S., Büchel, C., Buitelaar, J., Calhoun, V. D., Cannon, D. M., Cattrell, A., Cheng, Y., Conrod, P. J., Conzelmann, A., Corvin, A., Crespo-Facorro, B., Crivello, F., Dannlowski, U., De Zubicaray, G. I., De Zwarte, S. M., Deary, I. J., Desrivières, S., Doan, N. T., Donohoe, G., Dørum, E. S., Ehrlich, S., Espeseth, T., Fernández, G., Flor, H., Fouche, J.-P., Frouin, V., Fukunaga, M., Gallinat, J., Garavan, H., Gill, M., Suarez, A. G., Gowland, P., Grabe, H. J., Grotegerd, D., Gruber, O., Hagenaars, S., Hashimoto, R., Hauser, T. U., Heinz, A., Hibar, D. P., Hoekstra, P. J., Hoogman, M., Howells, F. M., Hu, H., Hulshoff Pol, H. E.., Huyser, C., Ittermann, B., Jahanshad, N., Jönsson, E. G., Jurk, S., Kahn, R. S., Kelly, S., Kraemer, B., Kugel, H., Kwon, J. S., Lemaitre, H., Lesch, K.-P., Lochner, C., Luciano, M., Marquand, A. F., Martin, N. G., Martínez-Zalacaín, I., Martinot, J.-L., Mataix-Cols, D., Mather, K., McDonald, C., McMahon, K. L., Medland, S. E., Menchón, J. M., Morris, D. W., Mothersill, O., Maniega, S. M., Mwangi, B., Nakamae, T., Nakao, T., Narayanaswaamy, J. C., Nees, F., Nordvik, J. E., Onnink, A. M. H., Opel, N., Ophoff, R., Martinot, M.-L.-P., Orfanos, D. P., Pauli, P., Paus, T., Poustka, L., Reddy, J. Y., Renteria, M. E., Roiz-Santiáñez, R., Roos, A., Royle, N. A., Sachdev, P., Sánchez-Juan, P., Schmaal, L., Schumann, G., Shumskaya, E., Smolka, M. N., Soares, J. C., Soriano-Mas, C., Stein, D. J., Strike, L. T., Toro, R., Turner, J. A., Tzourio-Mazoyer, N., Uhlmann, A., Valdés Hernández, M., Van den Heuvel, O. A., Van der Meer, D., Van Haren, N. E.., Veltman, D. J., Venkatasubramanian, G., Vetter, N. C., Vuletic, D., Walitza, S., Walter, H., Walton, E., Wang, Z., Wardlaw, J., Wen, W., Westlye, L. T., Whelan, R., Wittfeld, K., Wolfers, T., Wright, M. J., Xu, J., Xu, X., Yun, J.-Y., Zhao, J., Franke, B., Thompson, P. M., Glahn, D. C., Mazoyer, B., Fisher, S. E., & Francks, C. (2017). Human subcortical asymmetries in 15,847 people worldwide reveal effects of age and sex. Brain Imaging and Behavior, 11(5), 1497-1514. doi:10.1007/s11682-016-9629-z.
Abstract
The two hemispheres of the human brain differ functionally and structurally. Despite over a century of research, the extent to which brain asymmetry is influenced by sex, handedness, age, and genetic factors is still controversial. Here we present the largest ever analysis of subcortical brain asymmetries, in a harmonized multi-site study using meta-analysis methods. Volumetric asymmetry of seven subcortical structures was assessed in 15,847 MRI scans from 52 datasets worldwide. There were sex differences in the asymmetry of the globus pallidus and putamen. Heritability estimates, derived from 1170 subjects belonging to 71 extended pedigrees, revealed that additive genetic factors influenced the asymmetry of these two structures and that of the hippocampus and thalamus. Handedness had no detectable effect on subcortical asymmetries, even in this unprecedented sample size, but the asymmetry of the putamen varied with age. Genetic drivers of asymmetry in the hippocampus, thalamus and basal ganglia may affect variability in human cognition, including susceptibility to psychiatric disorders.Additional information
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Hibar, D. P., Adams, H. H. H., Jahanshad, N., Chauhan, G., Stein, J. L., Hofer, E., Rentería, M. E., Bis, J. C., Arias-Vasquez, A., Ikram, M. K., Desrivieres, S., Vernooij, M. W., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K., Aribisala, B. S., Armstrong, N. J., Athanasiu, L. and 312 moreHibar, D. P., Adams, H. H. H., Jahanshad, N., Chauhan, G., Stein, J. L., Hofer, E., Rentería, M. E., Bis, J. C., Arias-Vasquez, A., Ikram, M. K., Desrivieres, S., Vernooij, M. W., Abramovic, L., Alhusaini, S., Amin, N., Andersson, M., Arfanakis, K., Aribisala, B. S., Armstrong, N. J., Athanasiu, L., Axelsson, T., Beecham, A. H., Beiser, A., Bernard, M., Blanton, S. H., Bohlken, M. M., Boks, M. P., Bralten, J., Brickman, A. M., Carmichael, O., Chakravarty, M. M., Chen, Q., Ching, C. R. K., Chouraki, V., Cuellar-Partida, G., Crivello, F., den Brabander, A., Doan, N. T., Ehrlich, S., Giddaluru, S., Goldman, A. L., Gottesman, R. F., Grimm, O., Griswold, M. E., Guadalupe, T., Gutman, B. A., Hass, J., Haukvik, U. K., Hoehn, D., Holmes, A. J., Hoogman, M., Janowitz, D., Jia, T., Jørgensen, K. N., Mirza-Schreiber, N., Kasperaviciute, D., Kim, S., Klein, M., Krämer, B., Lee, P. H., Liewald, D. C. M., Lopez, L. M., Luciano, M., Macare, C., Marquand, A. F., Matarin, M., Mather, K. A., Mattheisen, M., McKay, D. R., Milaneschi, Y., Maniega, S. M., Nho, K., Nugent, A. C., Nyquist, P., Olde Loohuis, L. M., Oosterlaan, J., Papmeyer, M., Pirpamer, L., Pütz, B., Ramasamy, A., Richards, J. S., Risacher, S., Roiz-Santiañez, R., Rommelse, N., Ropele, S., Rose, E., Royle, N. A., Rundek, T., Sämann, P. G., Saremi, A., Satizabal, C. L., Schmaal, L., Schork, A. J., Shen, L., Shin, J., Shumskaya, E., Smith, A. V., Sprooten, E., Strike, L. T., Teumer, A., Tordesillas-Gutierrez, D., Toro, R., Trabzuni, D., Trompet, S., Vaidya, D., Van der Grond, J., Van der Lee, S. J., Van der Meer, D., Van Donkelaar, M. M. J., Van Eijk, K. R., van Erp, T. G. M., Van Rooij, D., Walton, E., Westlye, L. T., Whelan, C. D., Windham, B. G., Winkler, A. M., Wittfeld, K. M., Woldehawariat, G., Wolf, C., Wolfers, T., Yanek, L. R., Yang, J., Zijdenbos, A., Zwiers, M. P., Agartz, I., Almasy, L., Ames, D., Amouyel, P., Andreassen, O. A., Arepalli, S., Assareh, A. A., Barral, S., Bastin, M. E., Becker, D. M., Becker, J. T., Bennett, D. A., Blangero, J., Van Bokhoven, H., Boomsma, D. I., Brodaty, H., Brouwer, R. M., Brunner, H. G., Buckner, R. L., Buitelaar, J. K., Bulayeva, K. B., Cahn, W., Calhoun, V. D., Cannon, D. M., Cavalleri, G. L., Cheng, C.-Y., Cichon, S., Cookson, M. R., Corvin, A., Crespo-Facorro, B., Curran, J. E., Czisch, M., Dale, A. M., Davies, G. E., De Craen, A. J. M., De Geus, E. J. C., De Jager, P. L., De Zubicaray, G. i., Deary, I. J., Debette, S., DeCarli, C., Delanty, N., Depondt, C., DeStefano, A., Dillman, A., Djurovic, S., Donohoe, G., Drevets, W. C., Duggirala, R., Dyer, T. D., Enzinger, C., Erk, S., Espeseth, T., Fedko, I. O., Fernández, G., Ferrucci, L., Fisher, S. E., Fleischman, D. A., Ford, I., Fornage, M., Foroud, T. M., Fox, P. T., Francks, C., Fukunaga, M., Gibbs, J. R., Glahn, D. C., Gollub, R. L., Göring, H. H. H., Green, R. C., Gruber, O., Gudnason, V., Guelfi, S., Haberg, A. K., Hansell, N. K., Hardy, J., Hartman, C. A., Hashimoto, R., Hegenscheid, K., Heinz, A., Le Hellard, S., Hernandez, D. G., Heslenfeld, D. J., Ho, B.-C., Hoekstra, P. J., Hoffmann, W., Hofman, A., Holsboer, F., Homuth, G., Hosten, N., Hottenga, J.-J., Huentelman, M., Pol, H. E. H., Ikeda, M., Jack Jr., C. R., Jenkinson, M., Johnson, R., Jonsson, E. G., Jukema, J. W., Kahn, R. S., Kanai, R., Kloszewska, I., Knopman, D. S., Kochunov, P., Kwok, J. B., Lawrie, S. M., Lemaître, H., Liu, X., Longo, D. L., Lopez, O. L., Lovestone, S., Martinez, O., Martinot, J.-L., Mattay, V. S., McDonald, C., Mcintosh, A. M., McMahon, F., McMahon, K. L., Mecocci, P., Melle, I., Meyer-Lindenberg, A., Mohnke, S., Montgomery, G. W., Morris, D. W., Mosley, T. H., Mühleisen, T. W., Müller-Myhsok, B., Nalls, M. A., Nauck, M., Nichols, T. E., Niessen, W. J., Nöthen, M. M., Nyberg, L., Ohi, K., Olvera, R. L., Ophoff, R. A., Pandolfo, M., Paus, T., Pausova, Z., Penninx, B. W. J. H., Pike, G. B., Potkin, S. G., Psaty, B. M., Reppermund, S., Rietschel, M., Roffman, J. L., Romanczuk-Seiferth, N., Rotter, J. I., Ryten, M., Sacco, R. L., Sachdev, P. S., Saykin, A. J., Schmidt, R., Schmidt, H., Schofield, P. R., Sigursson, S., Simmons, A., Singleton, A., Sisodiya, S. M., Smith, C., Smoller, J. W., Soininen, H., Steen, V. M., Stott, D. J., Sussmann, J. E., Thalamuthu, A., Toga, A. W., Traynor, B. J., Troncoso, J., Tsolaki, M., Tzourio, C., Uitterlinden, A. G., Hernández, M. C. V., Van der Brug, M., Van der Lugt, A., Van der Wee, N. J. A., Van Haren, N. E. M., Van Tol, M.-J., Vardarajan, B. N., Vellas, B., Veltman, D. J., Völzke, H., Walter, H., Wardlaw, J. M., Wassink, T. H., Weale, M. e., Weinberger, D. R., Weiner, M., Wen, W., Westman, E., White, T., Wong, T. Y., Wright, C. B., Zielke, R. H., Zonderman, A. B., Martin, N. G., Van Duijn, C. M., Wright, M. J., Longstreth, W. W. T., Schumann, G., Grabe, H. J., Franke, B., Launer, L. J., Medland, S. E., Seshadri, S., Thompson, P. M., & Ikram, A. (2017). Novel genetic loci associated with hippocampal volume. Nature Communications, 8: 13624. doi:10.1038/ncomms13624.
Abstract
The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer’s disease (rg=−0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness. -
Kavaklioglu, T., Guadalupe, T., Zwiers, M., Marquand, A. F., Onnink, M., Shumskaya, E., Brunner, H., Fernandez, G., Fisher, S. E., & Francks, C. (2017). Structural asymmetries of the human cerebellum in relation to cerebral cortical asymmetries and handedness. Brain Structure and Function, 22, 1611-1623. doi:10.1007/s00429-016-1295-9.
Abstract
There is evidence that the human cerebellum is involved not only in motor control but also in other cognitive functions. Several studies have shown that language-related activation is lateralized toward the right cerebellar hemisphere in most people, in accordance with leftward cerebral cortical lateralization for language and a general contralaterality of cerebral–cerebellar activations. In terms of behavior, hand use elicits asymmetrical activation in the cerebellum, while hand preference is weakly associated with language lateralization. However, it is not known how, or whether, these functional relations are reflected in anatomy. We investigated volumetric gray matter asymmetries of cerebellar lobules in an MRI data set comprising 2226 subjects. We tested these cerebellar asymmetries for associations with handedness, and for correlations with cerebral cortical anatomical asymmetries of regions important for language or hand motor control, as defined by two different automated image analysis methods and brain atlases, and supplemented with extensive visual quality control. No significant associations of cerebellar asymmetries to handedness were found. Some significant associations of cerebellar lobular asymmetries to cerebral cortical asymmetries were found, but none of these correlations were greater than 0.14, and they were mostly method-/atlas-dependent. On the basis of this large and highly powered study, we conclude that there is no overt structural manifestation of cerebellar functional lateralization and connectivity, in respect of hand motor control or language laterality -
De Kovel, C. G. F., Lisgo, S., Karlebach, G., Ju, J., Cheng, G., Fisher, S. E., & Francks, C. (2017). Left-right asymmetry of maturation rates in human embryonic neural development. Biological Psychiatry, 82(3), 204-212. doi:10.1016/j.biopsych.2017.01.016.
Abstract
Background
Left-right asymmetry is a fundamental organizing feature of the human brain, and neuro-psychiatric disorders such as schizophrenia sometimes involve alterations of brain asymmetry. As early as 8 weeks post conception, the majority of human fetuses move their right arms more than their left arms, but because nerve fibre tracts are still descending from the forebrain at this stage, spinal-muscular asymmetries are likely to play an important developmental role.
Methods
We used RNA sequencing to measure gene expression levels in the left and right spinal cords, and left and right hindbrains, of 18 post-mortem human embryos aged 4-8 weeks post conception. Genes showing embryonic lateralization were tested for an enrichment of signals in genome-wide association data for schizophrenia.
Results
The left side of the embryonic spinal cord was found to mature faster than the right side. Both sides transitioned from transcriptional profiles associated with cell division and proliferation at earlier stages, to neuronal differentiation and function at later stages, but the two sides were not in synchrony (p = 2.2 E-161). The hindbrain showed a left-right mirrored pattern compared to the spinal cord, consistent with the well-known crossing over of function between these two structures. Genes that showed lateralization in the embryonic spinal cord were enriched for association signals with schizophrenia (p = 4.3 E-05).
Conclusions
These are the earliest-stage left-right differences of human neural development ever reported. Disruption of the lateralised developmental programme may play a role in the genetic susceptibility to schizophrenia.Additional information
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Ocklenburg, S., Schmitz, J., Moinfar, Z., Moser, D., Klose, R., Lor, S., Kunz, G., Tegenthoff, M., Faustmann, P., Francks, C., Epplen, J. T., Kumsta, R., & Güntürkün, O. (2017). Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries. eLife, 6: e22784. doi:10.7554/eLife.22784.001.
Abstract
Lateralization is a fundamental principle of nervous system organization but its molecular determinants are mostly unknown. In humans, asymmetric gene expression in the fetal cortex has been suggested as the molecular basis of handedness. However, human fetuses already show considerable asymmetries in arm movements before the motor cortex is functionally linked to the spinal cord, making it more likely that spinal gene expression asymmetries form the molecular basis of handedness. We analyzed genome-wide mRNA expression and DNA methylation in cervical and anterior thoracal spinal cord segments of five human fetuses and show development-dependent gene expression asymmetries. These gene expression asymmetries were epigenetically regulated by miRNA expression asymmetries in the TGF-β signaling pathway and lateralized methylation of CpG islands. Our findings suggest that molecular mechanisms for epigenetic regulation within the spinal cord constitute the starting point for handedness, implying a fundamental shift in our understanding of the ontogenesis of hemispheric asymmetries in humans -
Thompson, P. M., Andreassen, O. A., Arias-Vasquez, A., Bearden, C. E., Boedhoe, P. S., Brouwer, R. M., Buckner, R. L., Buitelaar, J. K., Bulaeva, K. B., Cannon, D. M., Cohen, R. A., Conrod, P. J., Dale, A. M., Deary, I. J., Dennis, E. L., De Reus, M. A., Desrivieres, S., Dima, D., Donohoe, G., Fisher, S. E. and 51 moreThompson, P. M., Andreassen, O. A., Arias-Vasquez, A., Bearden, C. E., Boedhoe, P. S., Brouwer, R. M., Buckner, R. L., Buitelaar, J. K., Bulaeva, K. B., Cannon, D. M., Cohen, R. A., Conrod, P. J., Dale, A. M., Deary, I. J., Dennis, E. L., De Reus, M. A., Desrivieres, S., Dima, D., Donohoe, G., Fisher, S. E., Fouche, J.-P., Francks, C., Frangou, S., Franke, B., Ganjgahi, H., Garavan, H., Glahn, D. C., Grabe, H. J., Guadalupe, T., Gutman, B. A., Hashimoto, R., Hibar, D. P., Holland, D., Hoogman, M., Pol, H. E. H., Hosten, N., Jahanshad, N., Kelly, S., Kochunov, P., Kremen, W. S., Lee, P. H., Mackey, S., Martin, N. G., Mazoyer, B., McDonald, C., Medland, S. E., Morey, R. A., Nichols, T. E., Paus, T., Pausova, Z., Schmaal, L., Schumann, G., Shen, L., Sisodiya, S. M., Smit, D. J., Smoller, J. W., Stein, D. J., Stein, J. L., Toro, R., Turner, J. A., Van den Heuvel, M., Van den Heuvel, O. A., Van Erp, T. G., Van Rooij, D., Veltman, D. J., Walter, H., Wang, Y., Wardlaw, J. M., Whelan, C. D., Wright, M. J., & Ye, J. (2017). ENIGMA and the Individual: Predicting Factors that Affect the Brain in 35 Countries Worldwide. NeuroImage, 145, 389-408. doi:10.1016/j.neuroimage.2015.11.057.
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Fisher, S. E., Francks, C., McCracken, J. T., McGough, J. J., Marlow, A. J., MacPhie, I. L., Newbury, D. F., Crawford, L. R., Palmer, C. G. S., Woodward, J. A., Del’Homme, M., Cantwell, D. P., Nelson, S. F., Monaco, A. P., & Smalley, S. L. (2002). A genomewide scan for loci involved in Attention-Deficit/Hyperactivity Disorder. American Journal of Human Genetics, 70(5), 1183-1196. doi:10.1086/340112.
Abstract
Attention deficit/hyperactivity disorder (ADHD) is a common heritable disorder with a childhood onset. Molecular genetic studies of ADHD have previously focused on examining the roles of specific candidate genes, primarily those involved in dopaminergic pathways. We have performed the first systematic genomewide linkage scan for loci influencing ADHD in 126 affected sib pairs, using a ∼10-cM grid of microsatellite markers. Allele-sharing linkage methods enabled us to exclude any loci with a λs of ⩾3 from 96% of the genome and those with a λs of ⩾2.5 from 91%, indicating that there is unlikely to be a major gene involved in ADHD susceptibility in our sample. Under a strict diagnostic scheme we could exclude all screened regions of the X chromosome for a locus-specific λs of ⩾2 in brother-brother pairs, demonstrating that the excess of affected males with ADHD is probably not attributable to a major X-linked effect. Qualitative trait maximum LOD score analyses pointed to a number of chromosomal sites that may contain genetic risk factors of moderate effect. None exceeded genomewide significance thresholds, but LOD scores were >1.5 for regions on 5p12, 10q26, 12q23, and 16p13. Quantitative-trait analysis of ADHD symptom counts implicated a region on 12p13 (maximum LOD 2.6) that also yielded a LOD >1 when qualitative methods were used. A survey of regions containing 36 genes that have been proposed as candidates for ADHD indicated that 29 of these genes, including DRD4 and DAT1, could be excluded for a λs of 2. Only three of the candidates—DRD5, 5HTT, and CALCYON—coincided with sites of positive linkage identified by our screen. Two of the regions highlighted in the present study, 2q24 and 16p13, coincided with the top linkage peaks reported by a recent genome-scan study of autistic sib pairs. -
Fisher, S. E., Francks, C., Marlow, A. J., MacPhie, I. L., Newbury, D. F., Cardon, L. R., Ishikawa-Brush, Y., Richardson, A. J., Talcott, J. B., Gayán, J., Olson, R. K., Pennington, B. F., Smith, S. D., DeFries, J. C., Stein, J. F., & Monaco, A. P. (2002). Independent genome-wide scans identify a chromosome 18 quantitative-trait locus influencing dyslexia. Nature Genetics, 30(1), 86-91. doi:10.1038/ng792.
Abstract
Developmental dyslexia is defined as a specific and significant impairment in reading ability that cannot be explained by deficits in intelligence, learning opportunity, motivation or sensory acuity. It is one of the most frequently diagnosed disorders in childhood, representing a major educational and social problem. It is well established that dyslexia is a significantly heritable trait with a neurobiological basis. The etiological mechanisms remain elusive, however, despite being the focus of intensive multidisciplinary research. All attempts to map quantitative-trait loci (QTLs) influencing dyslexia susceptibility have targeted specific chromosomal regions, so that inferences regarding genetic etiology have been made on the basis of very limited information. Here we present the first two complete QTL-based genome-wide scans for this trait, in large samples of families from the United Kingdom and United States. Using single-point analysis, linkage to marker D18S53 was independently identified as being one of the most significant results of the genome in each scan (P< or =0.0004 for single word-reading ability in each family sample). Multipoint analysis gave increased evidence of 18p11.2 linkage for single-word reading, yielding top empirical P values of 0.00001 (UK) and 0.0004 (US). Measures related to phonological and orthographic processing also showed linkage at this locus. We replicated linkage to 18p11.2 in a third independent sample of families (from the UK), in which the strongest evidence came from a phoneme-awareness measure (most significant P value=0.00004). A combined analysis of all UK families confirmed that this newly discovered 18p QTL is probably a general risk factor for dyslexia, influencing several reading-related processes. This is the first report of QTL-based genome-wide scanning for a human cognitive trait. -
Francks, C., Fisher, S. E., MacPhie, I. L., Richardson, A. J., Marlow, A. J., Stein, J. F., & Monaco, A. P. (2002). A genomewide linkage screen for relative hand skill in sibling pairs. American Journal of Human Genetics, 70(3), 800-805. doi:10.1086/339249.
Abstract
Genomewide quantitative-trait locus (QTL) linkage analysis was performed using a continuous measure of relative hand skill (PegQ) in a sample of 195 reading-disabled sibling pairs from the United Kingdom. This was the first genomewide screen for any measure related to handedness. The mean PegQ in the sample was equivalent to that of normative data, and PegQ was not correlated with tests of reading ability (correlations between −0.13 and 0.05). Relative hand skill could therefore be considered normal within the sample. A QTL on chromosome 2p11.2-12 yielded strong evidence for linkage to PegQ (empirical P=.00007), and another suggestive QTL on 17p11-q23 was also identified (empirical P=.002). The 2p11.2-12 locus was further analyzed in an independent sample of 143 reading-disabled sibling pairs, and this analysis yielded an empirical P=.13. Relative hand skill therefore is probably a complex multifactorial phenotype with a heterogeneous background, but nevertheless is amenable to QTL-based gene-mapping approaches.
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Francks, C., Fisher, S. E., Olson, R. K., Pennington, B. F., Smith, S. D., DeFries, J. C., & Monaco, A. P. (2002). Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus: Quantitative association analysis and positional candidate genes SEMA4F and OTX1. Psychiatric Genetics, 12(1), 35-41.
Abstract
A locus on chromosome 2p12-16 has been implicated in dyslexia susceptibility by two independent linkage studies, including our own study of 119 nuclear twin-based families, each with at least one reading-disabled child. Nonetheless, no variant of any gene has been reported to show association with dyslexia, and no consistent clinical evidence exists to identify candidate genes with any strong a priori logic. We used 21 microsatellite markers spanning 2p12-16 to refine our 1-LOD unit linkage support interval to 12cM between D2S337 and D2S286. Then, in quantitative association analysis, two microsatellites yielded P values<0.05 across a range of reading-related measures (D2S2378 and D2S2114). The exon/intron borders of two positional candidate genes within the region were characterized, and the exons were screened for polymorphisms. The genes were Semaphorin4F (SEMA4F), which encodes a protein involved in axonal growth cone guidance, and OTX1, encoding a homeodomain transcription factor involved in forebrain development. Two non-synonymous single nucleotide polymorphisms were found in SEMA4F, each with a heterozygosity of 0.03. One intronic single nucleotide polymorphism between exons 12 and 13 of SEMA4F was tested for quantitative association, but no significant association was found. Only one single nucleotide polymorphism was found in OTX1, which was exonic but silent. Our data therefore suggest that linkage with reading disability at 2p12-16 is not caused by coding variants of SEMA4F or OTX1. Our study outlines the approach necessary for the identification of genetic variants causing dyslexia susceptibility in an epidemiological population of dyslexics. -
Francks, C., MacPhie, I. L., & Monaco, A. P. (2002). The genetic basis of dyslexia. The Lancet Neurology, 1(8), 483-490. doi:10.1016/S1474-4422(02)00221-1.
Abstract
Dyslexia, a disorder of reading and spelling, is a heterogeneous neurological syndrome with a complex genetic and environmental aetiology. People with dyslexia differ in their individual profiles across a range of cognitive, physiological, and behavioural measures related to reading disability. Some or all of the subtypes of dyslexia might have partly or wholly distinct genetic causes. An understanding of the role of genetics in dyslexia could help to diagnose and treat susceptible children more effectively and rapidly than is currently possible and in ways that account for their individual disabilities. This knowledge will also give new insights into the neurobiology of reading and language cognition. Genetic linkage analysis has identified regions of the genome that might harbour inherited variants that cause reading disability. In particular, loci on chromosomes 6 and 18 have shown strong and replicable effects on reading abilities. These genomic regions contain tens or hundreds of candidate genes, and studies aimed at the identification of the specific causal genetic variants are underway. -
Marlow, A. J., Fisher, S. E., Richardson, A. J., Francks, C., Talcott, J. B., Monaco, A. P., Stein, J. F., & Cardon, L. R. (2002). Investigation of quantitative measures related to reading disability in a large sample of sib-pairs from the UK. Behavior Genetics, 31(2), 219-230. doi:10.1023/A:1010209629021.
Abstract
We describe a family-based sample of individuals with reading disability collected as part of a quantitative trait loci (QTL) mapping study. Eighty-nine nuclear families (135 independent sib-pairs) were identified through a single proband using a traditional discrepancy score of predicted/actual reading ability and a known family history. Eight correlated psychometric measures were administered to each sibling, including single word reading, spelling, similarities, matrices, spoonerisms, nonword and irregular word reading, and a pseudohomophone test. Summary statistics for each measure showed a reduced mean for the probands compared to the co-sibs, which in turn was lower than that of the population. This partial co-sib regression back to the mean indicates that the measures are influenced by familial factors and therefore, may be suitable for a mapping study. The variance of each of the measures remained largely unaffected, which is reassuring for the application of a QTL approach. Multivariate genetic analysis carried out to explore the relationship between the measures identified a common factor between the reading measures that accounted for 54% of the variance. Finally the familiality estimates (range 0.32–0.73) obtained for the reading measures including the common factor (0.68) supported their heritability. These findings demonstrate the viability of this sample for QTL mapping, and will assist in the interpretation of any subsequent linkage findings in an ongoing genome scan. -
Smalley, S. L., Kustanovich, V., Minassian, S. L., Stone, J. L., Ogdie, M. N., McGough, J. J., McCracken, J. T., MacPhie, I. L., Francks, C., Fisher, S. E., Cantor, R. M., Monaco, A. P., & Nelson, S. F. (2002). Genetic linkage of Attention-Deficit/Hyperactivity Disorder on chromosome 16p13, in a region implicated in autism. American Journal of Human Genetics, 71(4), 959-963. doi:10.1086/342732.
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is the most commonly diagnosed behavioral disorder in childhood and likely represents an extreme of normal behavior. ADHD significantly impacts learning in school-age children and leads to impaired functioning throughout the life span. There is strong evidence for a genetic etiology of the disorder, although putative alleles, principally in dopamine-related pathways suggested by candidate-gene studies, have very small effect sizes. We use affected-sib-pair analysis in 203 families to localize the first major susceptibility locus for ADHD to a 12-cM region on chromosome 16p13 (maximum LOD score 4.2; P=.000005), building upon an earlier genomewide scan of this disorder. The region overlaps that highlighted in three genome scans for autism, a disorder in which inattention and hyperactivity are common, and physically maps to a 7-Mb region on 16p13. These findings suggest that variations in a gene on 16p13 may contribute to common deficits found in both ADHD and autism.
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